In Gossypium raimondiie RefTrans V1, 545 million RNA-Seq reads from publicly available peer-reviewed G. raimondiie RNA-Seq data sets (Renny-Byfield et al, 2015 [SRP017133]; Renny-Byfield et al, 2014 [SRP017168]; Li et al, 2014 [SRP009820]; Rambani et al, 2014 [SRP028270]), and 63,577 ESTs, were downloaded from the NCBI Short Read Archive database and the NCBI dbEST database, respectively. The RNA-Seq reads and ESTs were assembled by using the Mainlab RefTrans pipeline (manuscript in preparation – details of pipeline provided ahead of publication on request). The RefTran sequences were functionally characterized by pairwise comparison using the BLASTX algorithm against the Swiss-Prot (UniProtKB/Swiss-Prot Release 2015_10) and TrEMBL (UniProtKB/TrEMBL Release 2015_10) protein databases. Information on the top 25 matches with an expectation (E) value of ≤ 1E-06 were recorded and stored in CottonGen together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made to Gossypium raimondiie RefTrans V1 using InterProScan at the EBI through Blast2GO. The transcriptome and associated annotation are available to download, search by name, keyword (functional description), or mapped location, and view on the genome through JBrowse.

Homology was determined using the BLASTx algorithm with an e-value cutoff of 1.0 e-6 for the Gossypium raimondiie RefTrans V1 vs. the Swiss-Prot (UniProtKB/Swiss-Prot Release 2015_10), TrEMBL(UniProtKB/TrEMBL Release 2015_10). Only the best match was kept.